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Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change

Citation

Beer, Marc et al. (2021), Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change, Dryad, Dataset, https://doi.org/10.5061/dryad.5dv41ns6w

Abstract

Understanding spatial patterns of genetic differentiation and local adaptation is critical in a period of rapid environmental change. Climate change and anthropogenic development have led to population declines and shifting geographic distributions in numerous species. The streamside salamander, Ambystoma barbouri, is an endemic amphibian with a small geographic range that predominantly inhabits small, ephemeral streams. As A. barbouri is listed as near-threatened by the IUCN, we describe range-wide patterns of genetic differentiation and adaptation to assess the species’ potential to respond to environmental change. We use outlier scans and genetic-environment association analyses to identify genomic variation putatively underlying local adaptation across the species’ geographic range. We find evidence for adaptation with a polygenic architecture and a set of candidate SNPs that identify genes putatively contributing to local adaptation. Our results build on earlier work that suggests that some A. barbouri populations are locally adapted despite evidence for asymmetric gene flow between the range core and periphery. Taken together, the body of work describing the evolutionary genetics of range limits in A. barbouri suggest that the species may be unlikely to respond naturally to environmental challenges through a range shift or in situ adaptation. We suggest that management efforts such as assisted migration may be necessary in the future.

Methods

The dataset contains sequencing data for 112 individuals of the streamside salamander (Ambystoma barbouri). Sample DNA was processed using double-digest restriction site-associated DNA sequencing (ddRADseq) using the restriction enzymes EcoRI and PstI. Due to the large genome size of A. barbouri, we included only 30 individuals in each of four final libraries to attempt to increase sequencing depth across individuals; two individuals from each of four sampling locations were duplicately sequenced in different libraries. The four libraries were sequenced on an Illumina Hiseq 2000 sequencing system at the University of Oregon Genomics Core Facility (gc3f.uoregon.edu), using single-end 100bp reads. Samples were demultiplexed using the Stacks version 2.52 module process_radtags with options -c -q -r enabled.

Usage Notes

The following files are present in this repository:
1) 120 gzipped fasta files.
Generally one fq.gz file per sample (two files for each of the eight duplicately sequenced samples).

2) sample_metadata.csv
Contains four fields: sample ID (prefixes on the fq.gz files), duplicate ID (if applicable), collection locality name, and sequencing lane.

3) location_coords.csv
Contains four fields: collection locality name, collection locality abbreviation (referenced in the associated publication), WGS84 decimal degree longitude, and WGS84 decimal degree latitude.

This information is also summarized in the README.txt file.

Funding

American Museum of Natural History, Award: Theodore Roosevelt Memorial Fund

Sigma Xi Grants-in-Aid, Award: G20130315163610

School of Biological Sciences, Washington State University, Award: Elling Endowment

National Science Foundation, Award: DEB-1501281

National Institutes of Health, Award: R01-GM126563

National Science Foundation Graduate Research Fellowship Program, Award: 1842493